Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Thiele, Sven; Cerone, Luca; Saez-Rodriguez, Julio; Siegel, Anne; Guziołowski, Carito; Klamt, Steffen
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: E. coli -- Gene regulation -- Interaction graphs -- Sign consistency -- Uncertainty -- Logic modeling -- Answer Set Programming (ASP); Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0733-7
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background A rapidly growing amount of knowledge about signaling and gene regulatory networks is available in databases such as KEGG, Reactome, or RegulonDB. There is an increasing need to relate this knowledge to high-throughput data in order to (in)validate network topologies or to decide which interactions are present or inactive in a given cell type under a particular environmental condition. Interaction graphs provide a suitable representation of cellular networks with information flows and methods based on sign consistency approaches have been shown to be valuable tools to (i) predict qualitative responses, (ii) to test the consistency of network topologies and experimental data, and (iii) to apply repair operations to the network model suggesting missing or wrong interactions. Results We present a framework to unify different notions of sign consistency and propose a refined method for data discretization that considers uncertainties in experimental profiles. We furthermore introduce a new constraint to filter undesired model behaviors induced by positive feedback loops. Finally, we generalize the way predictions can be made by the sign consistency approach. In particular, we distinguish strong predictions (e.g. increase of a node level) and weak predictions (e.g., node level increases or remains unchanged) enlarging the overall predictive power of the approach. We then demonstrate the applicability of our framework by confronting a large-scale gene regulatory network model ofEscherichia coli with high-throughput transcriptomic measurements. Conclusion Overall, our work enhances the flexibility and power of the sign consistency approach for the prediction of the behavior of signaling and gene regulatory networks and, more generally, for the validation and inference of these networks